Quinlan AR: BEDTools: The swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 47:11.12.1–34. 2014.PubMed/NCBIView Article:Google Scholar 45 Grabe N: AliBaba2: Context specific identification of transcription factor binding sites. In Silico Biol. 2 (Suppl):S1–15. 2002....
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal - GitHub - loosolab/TOBIAS: Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
DeepTFactor predicted 332 candidate TFs in Escherichia coli K-12 MG1655. Among them, 84 candidate TFs belong to the y-ome, which is a collection of genes that lack experimental evidence of function. We experimentally validated the results of DeepTFactor prediction by further characterizing genome...
The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This...
In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major Gramineae plants. DNA Res 2011;... K Mochida,T Yoshida,T Sakurai,... - 《Dna Research》 被引量: 203发表: 2009年 Editor's Choice: In Silico Analysis of Transcription ...
Such prediction models were constructed based on the compilation of known promoter sequences for each sigma factor. In E.coli, RegulonDB (5) contains both experimental and predicted cis- elements and is suited to the above-mentioned analyses while there are no databases containing comprehensive ...
In summary, DENIS is the first versatile framework for unbiased TF activity analysis via de novo motif generation and binding site assignment based on ATAC-seq footprinting. DENIS constitutes a versatile and cost effective tool when screening for a binding pattern of a factor that refuses detection...
The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (mod ENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely...
on Simulated Data. Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data.Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data.information theory
The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant ...